On 7/02/2011 9:52 PM, Qiong Zhang wrote:
Dear all gmx-users,
I have recently been testing the REMD simulations. I was running
simulations on a supercomputer systembased on the AMD Opteron 12-core
(2.1 GHz) processors. The Gromacs 4.5.3 version was used.
I have a system of 5172 atoms, of which 138 atoms belong to solute and
the other are water molecules. An exponential distribution of
temperatures was generated ranging from 276 to 515 K in total of 42
replicas or from 298 to 420 K in total of 24 replicas, ensuring that
the exchange ratio between all adjacent replicas is about 0.25. The
replica exchange was carried out every 0.5ps. The integrate step size
was 2fs.
For the above system, when REMD is simulated over 24 replicas, the
simulation speed is reasonably fast. However, when REMD is simulated
over 42 replicas, the simulation speed is awfully slow.Please see the
following table for the speed.
----------------------------------------------------------------------------
Replica numberCPU numberspeed
249658015steps/15minutes
4242865steps/15minutes
42841175steps/15minutes
421681875steps/15minutes
423362855steps/15minutes
The command line for the mdrun is:
aprun -n (CPU number here) mdrun_d -s md.tpr -multi (replica number
here) -replex 250
My questions are :
1) why the REMD for the 42 replicas is so slow for the same system?
2) On what aspects can I improve the operating efficiency please?
What's the network hardware? Can other machine load influence your
network performance?
Are the systems in the NVT ensemble? Use diff to check the .mdp files
differ only how you think they do.
What are the values of nstlist and nstcalcenergy?
Take a look at the execution time breakdown at the end of the .log
files, and do so for more than one replica. With the current
implementation, every simulation has to synchronize and communicate
every handful of steps, which means that large scale parallelism won't
work efficiently unless you have fast network hardware that is dedicated
to your job. This effect shows up in the "Rest" row of the time
breakdown. With Infiniband, I'd expect you should only be losing about
10% of the run time total. The 30-fold loss you have upon going from
24->42 replicas keeping 4 CPUs/replica suggests some other contribution,
however.
Mark
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